User: lkmklsmn
lkmklsmn • 930
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Posts by lkmklsmn
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... Hi biostars,
FASTQ files contain sequencing reads 'as they come off the sequencing instrument' (https://genome.ucsc.edu/ENCODE/fileFormats.html#FASTQ). Is there any particular order to them? E.g. based on the position of the flow cell? Quality?
Thanks in advance. ...
written 3.7 years ago by
lkmklsmn • 930
• updated
3.7 years ago by
Brian Bushnell ♦ 17k
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Comment:
C: ribosomal RNA contamination
... Thanks! Its true that some of the samples had low RINs. Is there any way to correct for this? And still use the samples. As of right now, PCA clustering does not reveal my treatment structure and I am worried these samples are unusable. ...
written 3.9 years ago by
lkmklsmn • 930
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... Hi,
I am working on a RNAseq data set of about 20 human tissue samples. However, some of the samples have a very low alignment rate (~30-40%) while the rest has a a decent alignment rate around 80%. I aligned the reads using STAR with default settings. The log file tells me that for those samples ...
written 3.9 years ago by
lkmklsmn • 930
• updated
3.9 years ago by
Devon Ryan ♦ 97k
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... Hi,
I am looking for some sort of database/compilation of RNA-seq data that allows me to quickly search by RNA-extraction protocol. More particular, I am interested in ALL GEO deposited RNA-seq datasets which extracted total RNA (as opposed to polyadenylated extraction protocols). Is there are lis ...
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Comment:
C: Ribosomal RNA in RNA-seq data
... Thanks. Yes the percentage of multi-mapping reads is very high in those affected samples. Given that only a subset of the samples are affected by this (Alignment rate<50%) my conclusion is that there must have been some error in the rRNA depletion step. ...
written 4.0 years ago by
lkmklsmn • 930
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... Hi biostars,
I am analyzing RNA-seq data (not for the first time) but for a subset of samples I am getting a very low alignment rate (~30%). To find out what is going on I have looked at some of the unaligned reads and they seem to come from ribosomal RNA.
Now my question: Are ribosomal RNA sequ ...
written 4.0 years ago by
lkmklsmn • 930
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... I find the pseudo alignment approach (kallisto, salmon, sailfish) very innovative. However, I would like to point out that RNA-seq data carries a lot more information than just gene expression levels. In my opinion the gene-level output of RNA-seq data is an alignment and not just an expression esti ...
written 4.6 years ago by
lkmklsmn • 930
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... I am using IGV to look at some RNA-seq alignment. In general I find this tool extremely helpful. However, when looking at some longer genes I am unable to visualize the alignment and I receive the message: "Zoom in to see alignment".
Is there a way to change this setting to visualize the entire ge ...
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... From the command line:
seq 1 n | paste bedfile - > bedfileWithInteger ...
written 4.6 years ago by
lkmklsmn • 930
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... Can I download gene expression data from ICGC? If so, how? Do I need controlled access? ...
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